User: harmadikemil

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Posts by harmadikemil

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Extract mitogenome from seqences
... Dear All! I have a big database, full of different sequences, most of it in fastq.gz files. (archaic and recent human sequences) My task is to extract the mitogenome sequences from them and reconstruct the mitogenome in one fasta. I have tried to map to MT ref genome, and remove all unmapped reads, ...
genome alignment mitogenome written 5 months ago by harmadikemil0
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Comment: C: Picard's Tool MarkDuplicates problem
... 2.21.3-SNAPSHOT is the Picard's version this is the whole log: ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ***** ...
written 7 months ago by harmadikemil0
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Picard's Tool MarkDuplicates problem
... Dear all! I try to use Picard's tool, but I always get an error code. I used the first version, and get a note (the tool didn't work after it). The second type of syntax i get an error code. What should be the solution for it? java -jar /data/tools/java/picard.jar MarkDuplicates I=PLEper56_MT ...
bioinformatics picard written 7 months ago by harmadikemil0
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Comment: C: Extract information from txt
... Thank you, it worked perfectly! I would have an another question. Can I make a list of sequences with grep? For example: Pasteurella multocida query: NB501791:62:HLKV3AFXY:3:11601:15774:10353 1:N:0:AAGCAGA query: NB501791:62:HLKV3AFXY:3:11601:15774:10353 1:N:0:AAGCAGA query: NB ...
written 11 months ago by harmadikemil0
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Extract information from txt
... Dear All! I have a txt with this kind of information: query: NB501791:62:HLKV3AFXY:4:21507:10794:16613 1:N:0:AAGCAGA match:gi|1548994288|gb|CP034492.1| Eukaryotic synthetic construct chromosome 14 >gi|1549096114|gb|CP034517 match:gi|1351431640|ref|XM_024231364.1| PREDICTED: Pongo ab ...
archeogenetics python sequence blast written 11 months ago by harmadikemil0
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Comment: C: How i can extract the first hit's title from blast XML-s
... Thank you for the fast aswer! I wrote a short code, but my problem, that i don't know how to reach the hit_num part in the xml. My code is: x=1 for record in NCBIXML.parse(open("full_result.xml")): if record.alignments: print("\n") print("query: %s" %record.q ...
written 11 months ago by harmadikemil0
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How i can extract the first hit's title from blast XML-s
... Dear All! i'm new to bioinformatics, and i'm working on an archeogenetics project. My first task, that in a genome part i should search the contaminating, non-human segments. It's a ~500 shotgun sequence. I would have two questions: -How could i print out just the first hits from the XML. -How c ...
python biopython written 12 months ago by harmadikemil0

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